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2 Answers
2

The destruction only happens once, it's instantaneous, and there's only one creature vulnerable to it when it happens.

610.1. A one-shot effect does something just once and doesn’t have a duration. Examples include dealing damage, destroying a permanent, putting a token onto the battlefield, and moving an object from one zone to another.

Think of it a state machine. There's only two game states in the scenario.

State 1: Timber Protector and some indestructible Treefolks are on the battlefield.

Action: Destroy all creatures.

State 2: Timber Protector is in the graveyard. Some Treefolks are on the battlefield.

This is an accurate model of Magic. Take triggered abilities, for example. They trigger based on the state of the game before the actions (if they are LTB triggers) or after the action (default), but not during. There is no "during" anywhere in Magic.
–
ikegamiFeb 23 at 20:07

700.4. If a permanent is indestructible, rules and effects can’t destroy it. (See rule 701.6, “Destroy.”) Such permanents are not destroyed by lethal damage, and they ignore the lethal-damage state-based action (see rule 704.5g). Rules or effects may cause an indestructible permanent to be sacrificed, put into a graveyard, or exiled.

700.4a Although the text “[This permanent] is indestructible” is an ability, actually being indestructible is neither an ability nor a characteristic. It’s just something that’s true about a permanent.

Therefore, as ikegami said above, all treefolk are indestructible when the Day of Judgement resolves except for the Timber Protector and survive, while the Timber Protector is destroyed and goes to the graveyard.

Now, if another board wipe occurs before you give them indestructibly or regeneration, then all of your treefolk are destroyed.

EDIT:

However, if you were to use a board sweeper such as Blasphemous Act instead all your creatures would be destroyed because then all creatures would have 13 damage marked on them, the Timber Protector would be destroyed because of damage, then all other treefolk would lose indestructibility and die because of lethal damage (which wouldn't leave the creature until the cleanup step).